Abstract: In September 2016, surface soils were collected in sample plots applied with no fertilizer (CK), pig manure alone, pig manure mixed with nitrogen fertilizer and pig manure mixed with nitrogen, phosphorus and potassium fertilizers for 13 years in Yanting Purple Soil Station of Agricultural Ecological Experiment in Sichuan province. Determinations on pathogenic bacterum were implemented by high-throughput sequencing. The results demonstrated that there were a total of 18 genera in the soil samples. Mycobacterium shamefaciens, Bacillus weidenstetten and Bacillus megaterium were the most prevalent, accounting for 45.5%-80.0% of the total abundance. M. shamefaciens could be detected in every sample. The results of principal co-ordinates analysis and one-way analysis showed that there were no significant differences of composition and abundance of pathogenic bacterium among plots with different fertilization treatments. The results of procrustes analysis and redundancy analyses indicated that soil physicochemical properties might be the important influencing factor for the composition of soil pathogenic bacterium.